Article
Quantification of rare allelic variants from pooled genomic DNA.
Nature methods - 1 Apr 2009
Druley Todd E, Vallania Francesco L M, Wegner Daniel J, Varley Katherine E, Knowles Olivia L, Bonds Jacqueline A, Robison Sarah W, Doniger Scott W, Hamvas Aaron, Cole F Sessions, Fay Justin C, Mitra Robi D
Abstract excerpt
We report a targeted, cost-effective method to quantify rare single-nucleotide polymorphisms from pooled human genomic DNA using second-generation sequencing. We pooled DNA from 1,111 individuals and targeted four genes to identify rare germline variants. Our base-calling algorithm, SNPSeeker, derived from large deviation theory, detected single-nucleotide polymorphisms present at frequencies below the raw error...
Topics
- Algorithms
- Base Sequence
- Chromosome Mapping
- DNA
- Gene Frequency
- Genetic Variation
- Molecular Sequence Data
- Polymorphism, Single Nucleotide
- Reproducibility of Results
- Sensitivity and Specificity